Just the stereo person here so this isn't my area of specialization but it does seem pretty simple. I would verify that there is a good ground cable of adequate gauge (2-ga.) with good connectors from the battery to engine block (and alternator mount via block or other essential connection). That loop has to be closed for operation. Connections can appear good but fall off with a mild tug. Also, corrosion is often concealed under a connector or insulating jacket.
Next, once the engine is running, lift the alternator feed. The boat should continue to run for a good while off well-charged batteries. But if you get no change in the reading then you know the alternator is not operational. Retrace all connections and then get the alternator diagnosed at a shop independent of the boat. If the alternator checks out you'll have to enlist a mechanic or take the boat in for service.

David
Earmark Marine